rs1326861

Variant names:

• chr20-53513125-A-C
• rs1326861

Your query was ambiguous. Multiple possible variants found:

• chr20-53513125-A-C
• chr20-53513125-A-G
• chr20-53513125-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.493 in 150,962 control chromosomes in the GnomAD database, including 18,542 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.49 (18542 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.280

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74414 AN: 150846 Hom.: 18522 Cov.: 28

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.600

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.484

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.493 AC: 74475 AN: 150962 Hom.: 18542 Cov.: 28 AF XY: 0.494 AC XY: 36421 AN XY: 73676

Gnomad4 AFR AF: 0.505

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.442

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.600

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.483

Alfa AF: 0.485 Hom.: 2789

Bravo AF: 0.485

Asia WGS AF: 0.432 AC: 1504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
DANN	Benign	0.39

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1326861; hg19: chr20-52129664;